The carrier proteome limit should be reassessed for each mass analyzer architecture

A clever utilization of classic proteomics reagents now allows the effective amplification of peptide sequencing potential in shotgun proteomics. The application of this method has helped usher in the exciting new field of single cell proteomics. While it was easy to first think that the discovery of Budnik et al., was finally the answer for protein PCR, limitations were carefully described by the authors and others. A study by Cheung et al., systematically identified the consequences of higher concentration carrier proteomes and defined the “carrier proteome limit”. While this work has been replicated by others, every analysis published to date has used a variation of the same mass analyzer. When the same analysis is performed on alternative instruments, these limits appear to be very different and attributable to defined characteristics of each mass analyzer. Specifically, in mass analyzers with higher relative intrascan linear dynamic range, increased carrier channels appear far less detrimental to quantitative accuracy. As such, we may be limiting the power of isobaric peptide signal “amplification” by restricting ourselves to traditional mass analyzer options.